oneChannelGUI
(last update 15/01/2010)
Window users:
Install ActiveTcl 8.4 or greater: www.activestate.com/Products/ActiveTcl/
Install R 2.10.0 (www.r-project.org).
The installation of latest Bioconductor with all packages needed for the course is done run an R shell and writing the following code:

source("http://bioconductor.org/biocLite.R")
biocLite(c("affy","AffyCompatible","affylmGUI","affyPLM","annaffy","annotate","AnnotationDbi",
                "beadarray","Biobase","biomaRt","Biostrings", "IRanges","DynDoc","genefilter","geneplotter","GenomeGraphs",
                "GO.db","GOstats","graph","hugene10sttranscriptcluster.db","hgu133a.db","hgu133a2.db","hgu133a2cdf",
                "hgu133a2probe","hgu133acdf","hgu133aprobe","hgu133plus2.db","hgu133plus2cdf","hgu133plus2probe",
                "hgu95av2cdf","hgu95av2probe","hugene10sttranscriptcluster.db","illuminaHumanv1BeadID.db",
                "illuminaHumanv2BeadID.db","illuminaHumanv3BeadID.db","IRanges","limma","maSigPro",
                "MergeMaid","metaArray","MiPP","mogene10sttranscriptcluster.db","multtest","oneChannelGUI",
                "org.Hs.eg.db","org.Mm.eg.db","org.Rn.eg.db","pamr","pdmclass","preprocessCore","R2HTML",
                "ragene10sttranscriptcluster.db","RankProd","RColorBrewer","Rgraphviz","rtracklayer","siggenes",
                "sizepower","ssize","tkrplot","tkWidgets","widgetTools","xtable", "HuExExonProbesetLocation",
                "MoExExonProbesetLocation",  "RaExExonProbesetLocation"))

When installation is finished.
  You can load the library(oneChannelGUI).
To start oneChannelGUI follow the instruction given int the first set of course slides or in the oneChannelGUI user guide.

Windows users:
For the correct installation of Rgraphviz , a library used for GO network visualization it is necessary:
1) Download and install Graphviz version 2.20.3.1
http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi
2) Add the location of the Graphviz binaries, the default being
C:\Program Files\Graphviz 2.21\bin, to your PATH system environment
variable.
3) Download and install the Rgraphviz package in R-2.10.0 using biocLite.
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
4) Restart R





ADDITIONAL INFORMATION
Affymetrix test data sets and exercises
oneChannelGUI tutorial and exercises 1st part
oneChannelGUI tutorial and exercises 2nd part
Set of data to test the functionalities of oneChannelGUI
3IVT two class unpaired test set to test oneChannelGUI statistical tests, filtering, etc.
Data set derved from processed data file from E-TABM-158 ArrayExpress data set to test oneChannelGUI classification modules
Two GEO data sets to test oneChannelGUI statistical tests, filtering, etc.
Tab delimited file data set, based on moe4302, to test oneChannelGUI statistical tests, filtering, etc
Time course data set to test maSigPro implementation of oneChannelGUI
Hs/Mm/Rat two class unpaired data sets to test oneChannelGUI exon modules